def makeRunnable(self, tempDir):
from toil.common import toilPackageDirPath
pickleFile = tempDir.getTempFile(".pickle")
fileHandle = open(pickleFile, 'w')
cPickle.dump(self, fileHandle, cPickle.HIGHEST_PROTOCOL)
fileHandle.close()
multijobexec = os.path.join(toilPackageDirPath(), "bin", "multijob")
jtPath = os.path.split(toilPackageDirPath())[0]
return "%s %s %s" % (multijobexec, pickleFile, jtPath)
def makeRunnable(self, tempDir):
from toil.common import toilPackageDirPath
pickleFile = tempDir.getTempFile(".pickle")
fileHandle = open(pickleFile, 'w')
cPickle.dump(self, fileHandle, cPickle.HIGHEST_PROTOCOL)
fileHandle.close()
multijobexec = os.path.join(toilPackageDirPath(), "bin", "multijob")
jtPath = os.path.split(toilPackageDirPath())[0]
return "%s %s %s" % (multijobexec, pickleFile, jtPath)
def testUtilsStatsSort(self):
"""
Tests the stats commands on a complete run of the stats test.
"""
# Get the sort command to run
toilCommandString = ("{self.sort} "
"{self.toilDir} "
"--logLevel=DEBUG "
"--fileToSort={self.tempFile} "
"--N {self.N} --stats "
"--retryCount 99".format(**locals()))
# Run the script for the first time
system(toilCommandString)
self.assertTrue(os.path.exists(self.toilDir))
# Check we can run 'toil stats'
rootPath = os.path.join(toilPackageDirPath(), "utils")
toilStatsString = ("{self.toilMain} stats "
"{self.toilDir} --pretty".format(**locals()))
system(toilStatsString)
# Check the file is properly sorted
with open(self.tempFile, 'r') as fileHandle:
l2 = fileHandle.readlines()
self.assertEquals(self.correctSort, l2)
def testToilStats_SortSimple(self):
"""
Tests the toilStats utility using the scriptTree_sort example.
"""
for test in xrange(self.testNo):
tempDir = getTempDirectory(os.getcwd())
tempFile = getTempFile(rootDir=tempDir)
outputFile = getTempFile(rootDir=tempDir)
toilDir = os.path.join(tempDir, "testToil")
lines = 10000
maxLineLength = 10
N = 1000
makeFileToSort(tempFile, lines, maxLineLength)
# Sort the file
rootPath = os.path.join(toilPackageDirPath(), "test", "sort")
system("{rootPath}/sort.py "
"--toil {toilDir} "
"--logLevel=DEBUG "
"--fileToSort={tempFile} "
"--N {N} --stats "
"--jobTime 0.5 "
"--retryCount 99".format(**locals()))
# Now get the stats
toilStats = self.getScriptPath('toilStats')
system("{toilStats} "
"--toil {toilDir} "
"--outputFile {outputFile}".format(**locals()))
# Cleanup
system("rm -rf %s" % tempDir)
def __init__(self, config, batchSystem, jobStore, toilState):
self.config = config
self.jobStore = jobStore
self.jobStoreString = config.jobStore
self.toilState = toilState
self.jobBatchSystemIDToJobStoreIDHash = {}
self.batchSystem = batchSystem
self.jobsIssued = 0
self.workerPath = os.path.join(toilPackageDirPath(), "worker.py")
self.reissueMissingJobs_missingHash = {} #Hash to store number of observed misses
def __init__(self, config, batchSystem, jobStore, toilState):
self.config = config
self.jobStore = jobStore
self.jobStoreString = config.jobStore
self.toilState = toilState
self.jobBatchSystemIDToJobStoreIDHash = {}
self.batchSystem = batchSystem
self.jobsIssued = 0
self.workerPath = os.path.join(toilPackageDirPath(), "worker.py")
self.reissueMissingJobs_missingHash = {
} #Hash to store number of observed misses
def _getUtilScriptPath(cls, script_name):
return os.path.join(toilPackageDirPath(), 'utils', script_name + '.py')
def sort(self):
return os.path.join(toilPackageDirPath(), "test", "sort", "sort.py")
def getScriptPath(self, script_name):
return os.path.join(toilPackageDirPath(), 'utils', script_name + '.py')
def _getUtilScriptPath(cls, script_name):
return os.path.join(toilPackageDirPath(), 'utils', script_name + '.py')
